Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012096.1 Corchorus capsularis cultivar CVL-1 contig12117, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 21422
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Found at i:2441 original size:21 final size:22
Alignment explanation
Indices: 2415--2466 Score: 79
Period size: 21 Copynumber: 2.4 Consensus size: 22
2405 TACGTATAAC
*
2415 AAAAAAAAAGCAGAAAAGTGA-
1 AAAAAAAAAGCAGAAAAGTAAT
*
2436 AAAAAAAAAGCAGAAACGTAAT
1 AAAAAAAAAGCAGAAAAGTAAT
2458 AAAAAAAAA
1 AAAAAAAAA
2467 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 19 0.68
22 9 0.32
ACGTcount: A:0.75, C:0.06, G:0.13, T:0.06
Consensus pattern (22 bp):
AAAAAAAAAGCAGAAAAGTAAT
Found at i:2494 original size:11 final size:12
Alignment explanation
Indices: 2458--2488 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2448 GAAACGTAAT
*
2458 AAAAAAAAATTA
1 AAAAAAAAATGA
2470 AAAAAAAAATGA
1 AAAAAAAAATGA
2482 AAAAAAA
1 AAAAAAA
2489 CAGAAACCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAAAAAAATGA
Found at i:2836 original size:12 final size:12
Alignment explanation
Indices: 2819--2867 Score: 62
Period size: 12 Copynumber: 4.0 Consensus size: 12
2809 ATGTTTTTCA
2819 AAAAAAAAAAGG
1 AAAAAAAAAAGG
*
2831 AAAAAAGAAAGG
1 AAAAAAAAAAGG
*
2843 AAGAAAAAAAGG
1 AAAAAAAAAAGG
*
2855 AAGAACAAAAAGG
1 AA-AAAAAAAAGG
2868 GAAATCACAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
12 23 0.74
13 8 0.26
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGG
Found at i:3783 original size:11 final size:11
Alignment explanation
Indices: 3767--3793 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3757 GAATATTCCT
3767 AAAAAAAAAGA
1 AAAAAAAAAGA
3778 AAAAAAAAAGA
1 AAAAAAAAAGA
3789 AAAAA
1 AAAAA
3794 TTAGGAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:4242 original size:11 final size:10
Alignment explanation
Indices: 4210--4252 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
4200 ATTGCTTCCC
*
4210 AAAAATTAAA
1 AAAAAATAAA
4220 AAAAAATAAA
1 AAAAAATAAA
4230 AAAAAATCCAAA
1 AAAAAAT--AAA
*
4242 AAAAGATAAA
1 AAAAAATAAA
4252 A
1 A
4253 GATGAAAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 20 0.69
12 9 0.31
ACGTcount: A:0.81, C:0.05, G:0.02, T:0.12
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:4260 original size:25 final size:22
Alignment explanation
Indices: 4217--4268 Score: 68
Period size: 22 Copynumber: 2.2 Consensus size: 22
4207 CCCAAAAATT
4217 AAAAAAAAATAAAAAAAAATCC
1 AAAAAAAAATAAAAAAAAATCC
*
4239 AAAAAAAGATAAAAGATGAAAATCC
1 AAAAAAAAATAAAA-A--AAAATCC
4264 AAAAA
1 AAAAA
4269 TTTTTAATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 13 0.50
23 1 0.04
25 12 0.46
ACGTcount: A:0.77, C:0.08, G:0.06, T:0.10
Consensus pattern (22 bp):
AAAAAAAAATAAAAAAAAATCC
Found at i:14672 original size:19 final size:18
Alignment explanation
Indices: 14639--14674 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14629 TTGAAATAAT
14639 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
14657 TCTTCAAATTATCTTCAA
1 TCTTC-AATGATCTTCAA
14675 GAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:15398 original size:13 final size:13
Alignment explanation
Indices: 15353--15399 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
15343 TATCATTTTA
15353 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
15366 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
15379 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
15393 CTCTTTT
1 CTCTTTT
15400 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:15408 original size:28 final size:27
Alignment explanation
Indices: 15350--15425 Score: 93
Period size: 27 Copynumber: 2.8 Consensus size: 27
15340 TTTTATCATT
15350 TTACTCTTTTCTTACTCTTTTTACTAA
1 TTACTCTTTTCTTACTCTTTTTACTAA
* *
15377 TTACTCTTTTCTTACTCTCTTTTATTTA
1 TTACTCTTTTCTTACTCT-TTTTACTAA
*
15405 TTAC-CACTTT-TTACTCTTTTT
1 TTACTC-TTTTCTTACTCTTTTT
15426 TTTTCTTATA
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
26 4 0.09
27 26 0.59
28 14 0.32
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (27 bp):
TTACTCTTTTCTTACTCTTTTTACTAA
Found at i:15595 original size:21 final size:21
Alignment explanation
Indices: 15547--15643 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
15537 TACTTTTTAA
*
15547 TGATTACCATTTTACTCTTTAC
1 TGATTACCATTTTGCTC-TTAC
* *
15569 TGATTACCATTTTGCTCTCAT
1 TGATTACCATTTTGCTCTTAC
15590 TGATTACCATTTTGCTCTTAC
1 TGATTACCATTTTGCTCTTAC
* * *
15611 TGATTACTATTTTACCTTTTAC
1 TGATTACCATTTT-GCTCTTAC
*
15633 TGATTATCATT
1 TGATTACCATT
15644 ACTTTTTACT
Statistics
Matches: 64, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
21 33 0.52
22 31 0.48
ACGTcount: A:0.22, C:0.21, G:0.07, T:0.51
Consensus pattern (21 bp):
TGATTACCATTTTGCTCTTAC
Found at i:15672 original size:21 final size:21
Alignment explanation
Indices: 15514--15673 Score: 130
Period size: 22 Copynumber: 7.5 Consensus size: 21
15504 CTTTATCATC
*
15514 TTACTCTTTACTGGTTACCTT
1 TTACTCTTTACTGATTACCTT
* *
15535 CTTACTTTTTAATGATTACCATT
1 -TTACTCTTTACTGATTACC-TT
15558 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACC-TT
* * *
15580 TTGCTC-TCATTGATTACCATT
1 TTACTCTTTACTGATTACC-TT
* *
15601 TTGCTC-TTACTGATTACTATT
1 TTACTCTTTACTGATTAC-CTT
* *
15622 TTAC-CTTTTACTGATTATC-A
1 TTACTC-TTTACTGATTACCTT
* *
15642 TTACTTTTTACTGATTACCCT
1 TTACTCTTTACTGATTACCTT
15663 TTACTCTTTAC
1 TTACTCTTTAC
15674 CATTCTTCCT
Statistics
Matches: 113, Mismatches: 19, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
20 17 0.15
21 43 0.38
22 51 0.45
23 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.06, T:0.51
Consensus pattern (21 bp):
TTACTCTTTACTGATTACCTT
Found at i:15700 original size:35 final size:35
Alignment explanation
Indices: 15648--15774 Score: 148
Period size: 35 Copynumber: 3.6 Consensus size: 35
15638 ATCATTACTT
* *
15648 TTTACTGATTACCCTTTACTCTTTACCATTCTTCC
1 TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
* *
15683 TTTACTGATTACTCTTTACTTTTTAGCATTCTTCT
1 TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
* *
15718 TTTACTGGTTACTCTTTACTTTTTTATCATT-TTACTC
1 TTTACTGATTACTCTTTAC-TTTTTACCATTCTT-C-C
* *
15755 TTTACTAATTACTCCTTACT
1 TTTACTGATTACTCTTTACT
15775 GATTATTCTT
Statistics
Matches: 79, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
35 51 0.65
36 12 0.15
37 16 0.20
ACGTcount: A:0.18, C:0.24, G:0.04, T:0.54
Consensus pattern (35 bp):
TTTACTGATTACTCTTTACTTTTTACCATTCTTCC
Found at i:15768 original size:14 final size:14
Alignment explanation
Indices: 15749--15788 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
15739 TTTTATCATT
15749 TTACTCTTTACTAA
1 TTACTCTTTACTAA
* *
15763 TTACTCCTTACTGA
1 TTACTCTTTACTAA
*
15777 TTATTCTTTACT
1 TTACTCTTTACT
15789 CTTTACCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.23, C:0.23, G:0.03, T:0.53
Consensus pattern (14 bp):
TTACTCTTTACTAA
Found at i:16063 original size:56 final size:53
Alignment explanation
Indices: 16001--16189 Score: 194
Period size: 47 Copynumber: 3.6 Consensus size: 53
15991 TATCAATTTA
* *
16001 CTGATTACTATCTTTTTACTTGATTACTGATTTACTAATTACTATTACCTTGACT
1 CTGATTAATCTCTTTTTAC-TGATTACTGATTTACTAATTAC-ATTACCTTGACT
* * * * *
16056 CTTGATTAATCTCTTCTTACTGATTTACTAATTGACTGATTACATTATCTTGACT
1 C-TGATTAATCTCTTTTTACTGA-TTACTGATTTACTAATTACATTACCTTGACT
*
16111 CTGATTAATCTCTTTTTACTGATTGACTGATTT-C------CATTGCCTTGACT
1 CTGATTAATCTCTTTTTACTGATT-ACTGATTTACTAATTACATTACCTTGACT
*
16158 TTGATTAATCTCTTTTTACTGATTTACTGATT
1 CTGATTAATCTCTTTTTACTGA-TTACTGATT
16190 GCCCCTTTTT
Statistics
Matches: 117, Mismatches: 13, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
47 39 0.33
48 2 0.02
53 3 0.03
54 26 0.22
55 16 0.14
56 31 0.26
ACGTcount: A:0.23, C:0.18, G:0.10, T:0.49
Consensus pattern (53 bp):
CTGATTAATCTCTTTTTACTGATTACTGATTTACTAATTACATTACCTTGACT
Found at i:17178 original size:50 final size:50
Alignment explanation
Indices: 17003--17229 Score: 226
Period size: 50 Copynumber: 4.5 Consensus size: 50
16993 CAAACTTCTA
* * *
17003 ATTCAAAGGTGACAT-TTTATTTCCTAATCACTTAAAAATTTAATCTTTT
1 ATTCAAAGGTGACATCTTTATTTACTAATTACTTAAAAATTCAATCTTTT
* * *
17052 ATTCAAAGGTTAAATCTTTATTTACCAATTACTCTAAAAATTCAATCTTTT
1 ATTCAAAGGTGACATCTTTATTTACTAATTACT-TAAAAATTCAATCTTTT
** * * *
17103 ACCCAATGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTT
1 ATTCAAAGGTGACATCTTTATTTACTAATTACTTAAAAATTCAATCTTTT
* * * **
17153 ATTCAAAGGTTACATCTTTACTTACTAACTCACTTGGAAA-TCTAAT-TTTT
1 ATTCAAAGGTGACATCTTTATTTACTAA-TTACTTAAAAATTC-AATCTTTT
* *
17203 TTGCTCAAAGGTGACATTTTTATTTAC
1 AT--TCAAAGGTGACATCTTTATTTAC
17230 AACATACTAA
Statistics
Matches: 144, Mismatches: 28, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
49 13 0.09
50 59 0.41
51 52 0.36
52 20 0.14
ACGTcount: A:0.34, C:0.16, G:0.07, T:0.44
Consensus pattern (50 bp):
ATTCAAAGGTGACATCTTTATTTACTAATTACTTAAAAATTCAATCTTTT
Found at i:17241 original size:101 final size:100
Alignment explanation
Indices: 17005--17244 Score: 263
Period size: 101 Copynumber: 2.4 Consensus size: 100
16995 AACTTCTAAT
* * *
17005 TCAAAGGTGACA-TTTTATTTCCTAATCACTTAAAAATTTAATCTTTTATTCAAAGGTTAAATCT
1 TCAAAGGTGACATTTTTATTTACAAAT-ACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
* *
17069 TTATTTACCAATTACTCTAAAAATTCAATCTTTTAC
65 TTACTTACCAATCACTCTAAAAATTCAATCTTTTAC
* * * * *
17105 CCAATGATGACATTTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTACATCT
1 TCAAAGGTGACATTTTTATTTAC-AAATACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
* ** * *
17170 TTACTTACTAACTCACT-TGGAAA-TCTAATTTTTTTGC
65 TTACTTACCAA-TCACTCTAAAAATTC-AA-TCTTTTAC
17207 TCAAAGGTGACATTTTTATTTACAACATAC-TAAAAATT
1 TCAAAGGTGACATTTTTATTTACAA-ATACTTAAAAATT
17245 TCTCCTTCTA
Statistics
Matches: 115, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
100 11 0.10
101 69 0.60
102 35 0.30
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.42
Consensus pattern (100 bp):
TCAAAGGTGACATTTTTATTTACAAATACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
TACTTACCAATCACTCTAAAAATTCAATCTTTTAC
Found at i:18285 original size:288 final size:287
Alignment explanation
Indices: 17741--18317 Score: 1084
Period size: 288 Copynumber: 2.0 Consensus size: 287
17731 TTTTTTCAAG
*
17741 TAAACTCGAAATCACAGCAAAATTTGAAGCTTTGCCGTGTAGAAGGAAGAAAAACAATGGAGAAA
1 TAAACCCGAAATCACAGCAAAATTTGAAGCTTTGCCGTGTAGAAGGAAGAAAAACAATGGAGAAA
17806 ATGGGGATAGCAGAGGGCTTTAAGACGATCCTCGAGCCTCTTGGCCTTCTCACGTCTCAAGTAAG
66 ATGGGGATAGCAGAGGGCTTTAAGACGATCCTCGAGCCTCTTGGCCTTCTCACGTCTCAAGTAAG
* *
17871 TCCCTTTCCTTTTACTCCCCTTTGTTGTTTTTTAGTTTTCAAAAAACCAGCCGAAAACCATGAAC
131 TCCCTTTCCTTTTACTCCCCTTTGTTGTTTTTTAGTTTACAAAAAACCAACCGAAAACCATGAAC
17936 CTCCTCCCCTCTTTTTTATAAACCCTAGTGGCCTCCTTTTAAATCCTCTGAAATGGGGTCTCCCT
196 CTCCTCCCCTCTTTTTTATAAACCCTAGTGGCCTCCTTTTAAATCCTCTGAAATGGGGTCTCCCT
18001 CCCTAGCTTTTGATTTCGACCCTCCTTT
261 -CCTAGCTTTTGATTTCGACCCTCCTTT
18029 TAAACCCGAAATCACAGCAAAATTTGAAGCTTTGCCGTGTAGAAGGAAGAAAAACAATGGAGAAA
1 TAAACCCGAAATCACAGCAAAATTTGAAGCTTTGCCGTGTAGAAGGAAGAAAAACAATGGAGAAA
18094 ATGGGGATAGCAGAGGGCTTTAAGACGATCCTCGAGCCTCTTGGCCTTCTCACGTCTCAAGTAAG
66 ATGGGGATAGCAGAGGGCTTTAAGACGATCCTCGAGCCTCTTGGCCTTCTCACGTCTCAAGTAAG
* *
18159 TCCCTTTCCTTTTACTCCCCTTTGTTGTTTTTTAGGTTTACATAAAACCAACTGAAAACCATGAA
131 TCCCTTTCCTTTTACTCCCCTTTGTTGTTTTTTA-GTTTACAAAAAACCAACCGAAAACCATGAA
18224 CCTCCTCCCCTCTTTTTTATAAACCCTAGTGGCCTCCTTTTAAATCCTCTGAAAT-GGGTCTCCC
195 CCTCCTCCCCTCTTTTTTATAAACCCTAGTGGCCTCCTTTTAAATCCTCTGAAATGGGGTCTCCC
18288 TCCTAGCTTTTGATTTCGACCCTCCTTT
260 TCCTAGCTTTTGATTTCGACCCTCCTTT
18316 TA
1 TA
18318 TTCTTCATCT
Statistics
Matches: 283, Mismatches: 5, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
287 29 0.10
288 173 0.61
289 81 0.29
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.31
Consensus pattern (287 bp):
TAAACCCGAAATCACAGCAAAATTTGAAGCTTTGCCGTGTAGAAGGAAGAAAAACAATGGAGAAA
ATGGGGATAGCAGAGGGCTTTAAGACGATCCTCGAGCCTCTTGGCCTTCTCACGTCTCAAGTAAG
TCCCTTTCCTTTTACTCCCCTTTGTTGTTTTTTAGTTTACAAAAAACCAACCGAAAACCATGAAC
CTCCTCCCCTCTTTTTTATAAACCCTAGTGGCCTCCTTTTAAATCCTCTGAAATGGGGTCTCCCT
CCTAGCTTTTGATTTCGACCCTCCTTT
Done.